X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwhatsNew.html;h=39ef82f1fc460d65c7c71428206cf72002eb3c3a;hb=6e23a164b465e79b78230d042159f4c8cc1fa9f0;hp=31b3f1f974e08a6ebe1750ac5af9387a806499f0;hpb=f7fd2fcf425c4a599dbb1440678672eb31cd865a;p=jalview.git
diff --git a/help/html/whatsNew.html b/help/html/whatsNew.html
index 31b3f1f..39ef82f 100755
--- a/help/html/whatsNew.html
+++ b/help/html/whatsNew.html
@@ -1,157 +1,199 @@
-
-
What's new ?
-
-What's new ?
-If you are reading this then you will already have seen some of the recent changes
- made to Jalview.
- Jalview takes advantage of some of the more recent user interface developments
- in the Java programming language. For instance Jalview is now a multi windowed
- application, this keeps all your Jalview windows neatly together in one main
- application window.
-If you were familiar with the original Jalview, here is a list of important
- features you should know about the current development:
-
- - Editing sequences is no longer the default when mouse clicking the alignment.
- Instead, mouse clicking on the alignment creates a "selection region"
- which may be full sequences or groups of residues.
- - To insert or edit the gaps in one sequence in alignment, the "Shift"
- key must be held down when dragging the mouse.
- - To insert or edit gaps for a group of sequences, the "Alt" key
- (or in X windows the "Control" key) must be held down.
- - Selecting colour schemes in the colour menu either sets just the "background"
- colourscheme for the alignment, or - when the tickbox "Apply colour to
- all groups" is ticked, applies the scheme to the background and all groups
- defined on the alignment.
- - Use the right mouse button (apple and click on the Mac) whilst the pointer
- is within the selection area to access the "define" region menu
- to define a new region, give it a name, and change its colourscheme and display
- properties.
- - Conservation is automatically updated whenever the alignment is edited
- - There is no "quick draw" option
- - Edits can be undone, and redone!
-
-
-
- Release |
- New Features |
- Issues Resolved |
-
-
- 2.07
- 7 /12/05 |
-
- - PDB Structure Viewer enhanced
- - Sequence Feature retrieval and display enhanced
- - Choose to output sequence start-end after sequence name for file output
- - Sequence Fetcher WSDBFetch@EBI
- |
-
- - HTML output writes groups and features
- - Group editing is Control and mouse click
- - Applet can read feature files, PDB files and can be used for HTML
- form input
- |
-
-
- 2.06
- 28/9/05 |
-
- - View annotations in wrapped mode
- - More options for PCA viewer
- |
-
- - GUI bugs resolved
- - Runs with -nodisplay from command line
- |
-
-
- 2.05b
- 15/9/05 |
-
- - Choose EPS export as lineart or text
- - Jar files are executable
- - Can read in Uracil - maps to unknown residue
- |
-
- - Known OutOfMemory errors give warning message
- - Overview window calculated more efficiently
- - Several GUI bugs resolved
- |
-
-
- 2.05
- 30/8/05 |
-
- - Edit and annotate in "Wrapped" view
- |
-
- - Several GUI bugs resolved
- |
-
-
- 2.04
- 24/8/05 |
-
- - Hold down mouse wheel & scroll to change font size
- |
-
- - Improved JPred client reliability
- - Improved loading of Jalview files
- |
-
-
- 2.03
- 18/8/05 |
-
- - Set Proxy server name and port in preferences
- - Multiple URL links from sequence ids
- - User Defined Colours can have a scheme name and added to Colour Menu
- - Choose to ignore gaps in consensus calculation
- - Unix users can set default web browser
- - Runs without GUI for batch processing
- - Dynamically generated Web Service Menus
- |
-
- - InstallAnywhere download for Sparc Solaris
- |
-
-
- 2.02
- 18/7/05 |
- |
-
- - Copy & Paste order of sequences maintains alignment order.
- |
-
-
- 2.01
- 12/7/05 |
-
- - Use delete key for deleting selection.
- - Use Mouse wheel to scroll sequences.
- - Help file updated to describe how to add alignment annotations.
- - Version and build date written to build properties file.
- - InstallAnywhere installation will check for updates at launch of Jalview.
- |
-
- - Delete gaps bug fixed.
- - FileChooser sorts columns.
- - Can remove groups one by one.
- - Filechooser icons installed.
- - Finder ignores return character when searching. Return key will initiate
- a search.
-
- |
-
-
- 2.0
- 20/6/05 |
- |
- |
-
-
-
-
-
+
+
+
+What's new ?
+
+
+
+ What's new ?
+
+ Jalview 2.8 includes a brand new logo, which you'll see in file
+ browsers, splash screens, and also on the new look Jalview site.
+
+ In addition to our new look, Jalview 2.8 includes a number of new
+ features.. some of which have been in development since July 2010. The
+ highlights are below, and - as usual, for a comprehensive list, take a
+ look at the Jalview 2.8 Release
+ Notes.
+
+
+ Highlights in Jalview Version 2.8
+
+
+ - Improved JABAWS client and new JABAWS 2.0 Services
+
+
+ - Support for RNA
+
+ - Import sequence and alignment associated WUSS or VIENNA dot-bracket
+ notation from files and the RFAM database
+ - Interactive editing of RNA secondary structure annotation
+ - Colour scheme for purine/pyrimidine and to highlight RNA
+ helices
+ - RNA canonical base pair consensus score and sequence logo
+ - Embedded VARNA RNA
+ secondary structure viewer in the Desktop
+
+
+ - Parse and display T-COFFEE alignment quality scores (thanks to Paolo Tomassi of the Notredame Group)
+ - Per sequence alignment annotation shading
+ - Enhanced PCA viewer: more export options, and switch between
+ different PCA modes and residue score models
+ - New Jalview Desktop database fetcher GUI
+ - Support for DAS 1.6 and DAS 2.0 sources (thanks to new JDAS Distributed Annotation client library)
+ - Export sequence database annotation as HTML report
+ - Normalised Sequence Logo Display
+
+
+ Issues Resolved (a select list - see the release history for full details)
+
+
+
+ Issues in the Jalview Desktop
+
+ - PDB, Unprot and EMBL (ENA) databases retrieved via wsdbfetch
+ REST service
+
+ -
+
+ Stop
+ windows being moved outside desktop on OSX
+
+ -
+ Filetype
+ associations not installed for webstart launch
+
+ -
+ Jalview
+ does not always retrieve progress of a JABAWS job execution in full
+ once it is complete
+
+ -
+ View
+ all structures superposed fails with exception
+
+ -
+ Jnet
+ job queues forever if a very short sequence is submitted for
+ prediction
+
+ -
+ Structure
+ view highlighting doesn't work on windows 7
+
+ -
+ Jalview
+ desktop fails to launch with exception when using proxy
+
+ -
+ Tree
+ calculation reports 'you must have 2 or more sequences
+ selected' when selection is empty
+
+ -
+ DAS
+ Sequence retrieval with range qualification results in sequence xref
+ which includes range qualification
+
+ -
+ Cannot
+ close news reader when JABAWS server warning dialog is shown
+
+ -
+ Edited
+ sequence not submitted to web service
+
+ -
+ Jalview
+ 2.7 Webstart and InstallAnywhere installer doesn't unpack and run
+ on OSX Mountain Lion
+
+ - The workaround for webstart is to go into the Security
+ panel (gatekeeper symbol) under System settings, and select the
+ 'allow any code to run' setting.
+
+
+ -
+ Annotation
+ panel not given a scroll bar when sequences with alignment annotation
+ are pasted into the alignment
+
+ -
+ Sequence
+ associated annotation rows not associated when loaded from jalview
+ project
+
+ -
+ Exceptions
+ when copy/paste sequences with grouped annotation rows to new window
+
+ -
+ Browser
+ launch fails with NPE on java 1.7
+
+
+
+
+ Issues specific to the JalviewLite Applet
+
+ -
+ Sequence
+ features are momentarily displayed before they are hidden using
+ hidefeaturegroups applet parameter
+
+ -
+ loading
+ features via javascript API automatically enables feature display
+
+ -
+ scrollToColumnIn
+ javascript API method doesn't work
+
+
+ Issues affecting both applet and application
+
+ -
+ Redundancy
+ removal fails for rna alignment
+
+ -
+ PCA
+ window shows grey box when first opened on OSX
+
+ -
+ Letters
+ coloured pink in sequence logo when alignment coloured with clustalx
+
+ -
+ Choosing
+ fonts without letter symbols defined causes exceptions and redraw
+ errors
+
+ -
+ Initial
+ PCA plot view is not same as manually reconfigured view
+
+
+
+